Then why even attempt to recover the Ba'ku with transporter tags? If they'd skipped that step, then they would have launched the collector and harvested the radiation...

That's what I'm saying. The only reason the So'na involved the Federation at all was because Ru'afo thought that would mitigate any risk of an armed confrontation with them. It's not like he worried about the Ba'ku putting up a fight, since he could just start the harvester and not even care what happened to them.

At the end of the day, its a movie that really makes little sense. Definitely had too many cooks in the kitchen and a weak director who didn't have the balls to ask for a rewrite.

The main thing that makes no sense is the Federation stepping into this situation at all. The Council should've told Ru'afo and his thugs to fuck off and not be caught anywhere near the Briar Patch, lest a Federation task force forcibly "remove" them. What we got instead was a Federation Council apparently dazzled by promises of immortality sold by one of the slimiest characters (figuratively and literally) ever put to film. It also involves a pretext in which the Federation deliberately violates the Prime Directive in order to benefit Federation citizens, which is one of the things the PD is specifically supposed to prevent.